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ShixiangWang / DoAbsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package
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Error message: the condition has length > 1 #33

Closed LoRner22 closed 4 months ago

LoRner22 commented 4 months ago

Dear sir, This error occured when I was use the test data，which also occurred when I tried to use ABSOLUTE to analyze single data. I had checked my input data，but I couldn't find something wrong. my code :


devtools::install_github("ShixiangWang/DoAbsolute")
library(DoAbsolute)
example_path = system.file("extdata", package = "DoAbsolute", mustWork = T)
library(data.table)
#segmentation文件
seg_normal =  file.path(example_path, "SNP6_blood_normal.seg.txt")
seg_solid  =  file.path(example_path, "SNP6_solid_tumor.seg.txt")
seg_metastatic  = file.path(example_path, "SNP6_metastatic_tumor.seg.txt")

maf_solid  = file.path(example_path, "solid_tumor.maf.txt")
maf_metastatic  = file.path(example_path, "metastatic_tumor.maf.txt")

seg_normal = fread(seg_normal)
seg_solid = fread(seg_solid)
seg_metastatic = fread(seg_metastatic)
maf_solid = fread(maf_solid)
maf_metastatic = fread(maf_metastatic)

Seg = Reduce(rbind, list(seg_normal, seg_solid, seg_metastatic))
Maf = Reduce(rbind, list(maf_solid, maf_metastatic))
Seg$Sample = substr(Seg$Sample, 1, 15)
Maf$Tumor_Sample_Barcode = substr(Maf$Tumor_Sample_Barcode, 1, 15) 

DoAbsolute(Seg = Seg, Maf = Maf,
           platform = "SNP_6.0",
           copy.num.type = "total",
           results.dir = "./a",
           nThread = 2,
           keepAllResult = TRUE,
           verbose = TRUE)

Seg: image Maf: image

Looking forward to your reply. Sincerely, Jesson Miao.

ShixiangWang commented 4 months ago

@LoRner22 Have you installed the ABSOLUTE with the following way?

install.packages("numDeriv")
path_to_file = system.file("extdata", "ABSOLUTE_1.0.6.tar.gz", package = "DoAbsolute", mustWork = T)
install.packages(path_to_file, repos = NULL, type="source")
LoRner22 commented 4 months ago

Thanks for your reply. Sure,sir.And the two packages could be loaded successfully.

---- Replied Message ---- | From | Shixiang Wang @.> | | Date | 05/05/2024 10:52 | | To | ShixiangWang/DoAbsolute @.> | | Cc | Jesson @.>, Mention @.> | | Subject | Re: [ShixiangWang/DoAbsolute] Error message: the condition has length > 1 (Issue #33) |

@LoRner22 Have you installed the ABSOLUTE with the following way?

install.packages("numDeriv") path_to_file= system.file("extdata", "ABSOLUTE_1.0.6.tar.gz", package="DoAbsolute", mustWork=T) install.packages(path_to_file, repos=NULL, type="source")

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ShixiangWang commented 4 months ago

What's your R version? Could you provide your R session?

devtools::session_info()
LoRner22 commented 4 months ago

I have tired the version 4.4.0，4.3.1 and 4.2.1，but the same error occurred. Is there a need for a even lower version？

---- Replied Message ---- | From | Shixiang Wang @.> | | Date | 05/05/2024 12:27 | | To | ShixiangWang/DoAbsolute @.> | | Cc | Jesson @.>, Mention @.> | | Subject | Re: [ShixiangWang/DoAbsolute] Error message: the condition has length > 1 (Issue #33) |

What's your R version? Could you provide your R session?

devtools::session_info()

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ShixiangWang commented 4 months ago

Should work >4.0. I just tried in my MacBook pro, but it just fine.

devtools::install_github("ShixiangWang/DoAbsolute")

install.packages("numDeriv")
path_to_file = system.file("extdata", "ABSOLUTE_1.0.6.tar.gz", package = "DoAbsolute", mustWork = T)
install.packages(path_to_file, repos = NULL, type="source")

library(DoAbsolute)

example_path = system.file("extdata", package = "DoAbsolute", mustWork = T)

library(data.table)
# Load Test Data ----------------------------------------------------------

# segmentation file
seg_normal =  file.path(example_path, "SNP6_blood_normal.seg.txt")
seg_solid  =  file.path(example_path, "SNP6_solid_tumor.seg.txt")
seg_metastatic  = file.path(example_path, "SNP6_metastatic_tumor.seg.txt")
# MAF file
maf_solid  = file.path(example_path, "solid_tumor.maf.txt")
maf_metastatic  = file.path(example_path, "metastatic_tumor.maf.txt")

# read data
seg_normal = fread(seg_normal)
seg_solid = fread(seg_solid)
seg_metastatic = fread(seg_metastatic)
maf_solid = fread(maf_solid)
maf_metastatic = fread(maf_metastatic)

# merge data
Seg = Reduce(rbind, list(seg_normal, seg_solid, seg_metastatic))
Maf = Reduce(rbind, list(maf_solid, maf_metastatic))

Seg$Sample = substr(Seg$Sample, 1, 15)
Maf$Tumor_Sample_Barcode = substr(Maf$Tumor_Sample_Barcode, 1, 15)

# test function
DoAbsolute(Seg = Seg, Maf = Maf, platform = "SNP_6.0", copy.num.type = "total",
           results.dir = "test", keepAllResult = TRUE, verbose = TRUE)

devtools::session_info()
ShixiangWang commented 4 months ago

Would you mind run the code above once again, and paste here anything printing to the R console?

LoRner22 commented 4 months ago

Dear Wang, I have run the code.The print information on the console was too long to recall so I could only copy some ending of them.(paste to the p.txt) This time it works,producing corresponding files:

Also,I have tried to drop the R version to 4.0.5.The error under the former versions I used disappeared.All my own 24 datas worked successfully.So strange.

xujie_miao

@. | ---- Replied Message ---- | From | Shixiang Wang @.> | | Date | 5/5/2024 12:42 | | To | @.> | | Cc | Jesson @.> , @.***> | | Subject | Re: [ShixiangWang/DoAbsolute] Error message: the condition has length > 1 (Issue #33) |

Would you mind run the code above once again, and paste here anything printing to the R console?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

$SC Pr_subclonal 0.08360404

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.41353 0.43430 0.07457 0.02762 0.01719 0.00404 0.00293 0.00293 0.00293 0.00293 0.00293 0.00293 0.00294 0.00530 0.00293 $SM Pr_somatic_clonal 0.8959114

$GL [1] 0

$SC Pr_subclonal 0.1040886

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.46134 0.46705 0.01611 0.02306 0.00274 0.00274 0.00274 0.00274 0.00274 0.00274 0.00507 0.00274 0.00274 0.00274 0.00274 $SM Pr_somatic_clonal 0.8573447

$GL [1] 0

$SC Pr_subclonal 0.1426553

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.39434 0.42016 0.07587 0.05733 0.00688 0.01379 0.00320 0.00320 0.00320 0.00320 0.00320 0.00320 0.00321 0.00600 0.00320 $SM Pr_somatic_clonal 0.9131441

$GL [1] 0

$SC Pr_subclonal 0.08685587

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.55796 0.37670 0.02191 0.01112 0.00282 0.00269 0.00269 0.00269 0.00270 0.00526 0.00269 0.00269 0.00269 0.00269 0.00269 $SM Pr_somatic_clonal 0.7794858

$GL [1] 0

$SC Pr_subclonal 0.2205142

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.66425 0.28187 0.01178 0.00328 0.00328 0.00328 0.00328 0.00328 0.00605 0.00328 0.00328 0.00328 0.00328 0.00328 0.00328 $SM Pr_somatic_clonal 0.830015

$GL [1] 0

$SC Pr_subclonal 0.169985

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.70460 0.25463 0.00298 0.00298 0.00298 0.00298 0.00506 0.00298 0.00298 0.00298 0.00298 0.00298 0.00298 0.00298 0.00298 $SM Pr_somatic_clonal 0.7731267

$GL [1] 0

$SC Pr_subclonal 0.2268733

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.75330 0.19952 0.00355 0.00355 0.00355 0.00461 0.00355 0.00355 0.00355 0.00355 0.00355 0.00355 0.00355 0.00355 0.00355 $SM Pr_somatic_clonal 0.7140579

$GL [1] 0

$SC Pr_subclonal 0.2859421

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.78338 0.17359 0.00312 0.00312 0.00560 0.00312 0.00312 0.00312 0.00312 0.00312 0.00312 0.00312 0.00312 0.00312 0.00312 $SM Pr_somatic_clonal 0.6288193

$GL [1] 0

$SC Pr_subclonal 0.3711807

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.76735 0.18160 0.00370 0.00370 0.00659 0.00370 0.00370 0.00370 0.00370 0.00370 0.00370 0.00370 0.00370 0.00370 0.00370 $SM Pr_somatic_clonal 0.6290502

$GL [1] 0

$SC Pr_subclonal 0.3709498

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.76152 0.18838 0.00364 0.00364 0.00638 0.00364 0.00364 0.00364 0.00364 0.00364 0.00364 0.00364 0.00364 0.00364 0.00364 $SM Pr_somatic_clonal 0.6582465

$GL [1] 0

$SC Pr_subclonal 0.3417535

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.73814 0.20395 0.00795 0.00416 0.00416 0.00416 0.00416 0.00416 0.00416 0.00416 0.00416 0.00416 0.00416 0.00416 0.00416 $SM Pr_somatic_clonal 0.4485609

$GL [1] 0

$SC Pr_subclonal 0.5514391

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.75209 0.19337 0.00718 0.00395 0.00395 0.00395 0.00395 0.00395 0.00395 0.00395 0.00395 0.00395 0.00395 0.00395 0.00395 $SM Pr_somatic_clonal 0.3617026

$GL [1] 0

$SC Pr_subclonal 0.6382974

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.39025 0.41246 0.07351 0.06016 0.01406 0.01428 0.00585 0.00331 0.00331 0.00331 0.00331 0.00331 0.00331 0.00622 0.00331 $SM Pr_somatic_clonal 0.919462

$GL [1] 0

$SC Pr_subclonal 0.08053798

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.44925 0.43093 0.04796 0.00798 0.02510 0.00357 0.00356 0.00356 0.00356 0.00356 0.00356 0.00356 0.00356 0.00670 0.00356 $SM Pr_somatic_clonal 0.901249

$GL [1] 0

$SC Pr_subclonal 0.09875099

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.45442 0.43567 0.04540 0.00848 0.01944 0.00336 0.00336 0.00336 0.00336 0.00336 0.00336 0.00336 0.00337 0.00631 0.00336 $SM Pr_somatic_clonal 0.8964434

$GL [1] 0

$SC Pr_subclonal 0.1035566

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.47029 0.45911 0.00896 0.02377 0.00320 0.00320 0.00320 0.00320 0.00320 0.00320 0.00320 0.00320 0.00320 0.00590 0.00320 $SM Pr_somatic_clonal 0.8849186

$GL [1] 0

$SC Pr_subclonal 0.1150814

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.63443 0.30937 0.01489 0.00344 0.00344 0.00344 0.00344 0.00344 0.00344 0.00344 0.00344 0.00344 0.00344 0.00344 0.00344 $SM Pr_somatic_clonal 0.8438519

$GL [1] 0

$SC Pr_subclonal 0.1561481

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.68926 0.26087 0.01079 0.00305 0.00305 0.00305 0.00305 0.00305 0.00554 0.00305 0.00305 0.00305 0.00305 0.00305 0.00305 $SM Pr_somatic_clonal 0.81374

$GL [1] 0

$SC Pr_subclonal 0.18626

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.70474 0.25617 0.00312 0.00300 0.00300 0.00300 0.00300 0.00300 0.00300 0.00300 0.00300 0.00300 0.00300 0.00300 0.00300 $SM Pr_somatic_clonal 0.7792655

$GL [1] 0

$SC Pr_subclonal 0.2207345

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.74944 0.20402 0.00358 0.00358 0.00358 0.00358 0.00358 0.00358 0.00358 0.00358 0.00358 0.00358 0.00358 0.00358 0.00358 $SM Pr_somatic_clonal 0.7382502

$GL [1] 0

$SC Pr_subclonal 0.2617498

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.69739 0.23916 0.00488 0.00488 0.00488 0.00488 0.00488 0.00488 0.00488 0.00488 0.00488 0.00488 0.00488 0.00488 0.00488 $SM Pr_somatic_clonal 0.5596631

$GL [1] 0

$SC Pr_subclonal 0.4403369

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.68212 0.25123 0.00513 0.00513 0.00513 0.00513 0.00513 0.00513 0.00513 0.00513 0.00513 0.00513 0.00513 0.00513 0.00513 $SM Pr_somatic_clonal 0.5790453

$GL [1] 0

$SC Pr_subclonal 0.4209547

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.76842 0.18079 0.00369 0.00369 0.00652 0.00369 0.00369 0.00369 0.00369 0.00369 0.00369 0.00369 0.00369 0.00369 0.00369 $SM Pr_somatic_clonal 0.6435261

$GL [1] 0

$SC Pr_subclonal 0.3564739

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.46302 0.43536 0.03692 0.02088 0.01424 0.00271 0.00271 0.00271 0.00271 0.00271 0.00271 0.00522 0.00271 0.00271 0.00271 $SM Pr_somatic_clonal 0.8562837

$GL [1] 0

$SC Pr_subclonal 0.1437163

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.58882 0.34389 0.01895 0.00373 0.00373 0.00373 0.00373 0.00373 0.00373 0.00373 0.00374 0.00726 0.00373 0.00373 0.00373 $SM Pr_somatic_clonal 0.8649597

$GL [1] 0

$SC Pr_subclonal 0.1350403

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.57573 0.37288 0.01644 0.00489 0.00273 0.00273 0.00273 0.00273 0.00273 0.00273 0.00273 0.00273 0.00273 0.00273 0.00273 $SM Pr_somatic_clonal 0.7664361

$GL [1] 0

$SC Pr_subclonal 0.2335639

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.76184 0.19693 0.00304 0.00304 0.00304 0.00304 0.00470 0.00304 0.00304 0.00304 0.00304 0.00304 0.00304 0.00304 0.00304 $SM Pr_somatic_clonal 0.718349

$GL [1] 0

$SC Pr_subclonal 0.281651

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.44919 0.42790 0.04846 0.00797 0.02621 0.00415 0.00366 0.00366 0.00366 0.00366 0.00366 0.00366 0.00366 0.00687 0.00366 $SM Pr_somatic_clonal 0.9041641

$GL [1] 0

$SC Pr_subclonal 0.09583594

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.36907 0.35486 0.02432 0.06110 0.07139 0.04486 0.02809 0.01410 0.00598 0.00679 0.00331 0.00331 0.00331 0.00619 0.00331 $SM Pr_somatic_clonal 0.9321067

$GL [1] 0

$SC Pr_subclonal 0.06789334

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.49748 0.41563 0.02086 0.02742 0.00958 0.00278 0.00266 0.00266 0.00266 0.00266 0.00277 0.00486 0.00266 0.00266 0.00266 $SM Pr_somatic_clonal 0.8304358

$GL [1] 0

$SC Pr_subclonal 0.1695642

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.73112 0.22485 0.00317 0.00317 0.00597 0.00317 0.00317 0.00317 0.00317 0.00317 0.00317 0.00317 0.00317 0.00317 0.00317 $SM Pr_somatic_clonal 0.5457939

$GL [1] 0

$SC Pr_subclonal 0.4542061

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.41798 0.42242 0.04603 0.03625 0.02627 0.01997 0.00605 0.00296 0.00280 0.00280 0.00280 0.00306 0.00499 0.00280 0.00280 $SM Pr_somatic_clonal 0.8872751

$GL [1] 0

$SC Pr_subclonal 0.1127249

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.42485 0.43229 0.03885 0.03026 0.02817 0.01697 0.00426 0.00275 0.00274 0.00274 0.00275 0.00300 0.00489 0.00274 0.00274 $SM Pr_somatic_clonal 0.8810088

$GL [1] 0

$SC Pr_subclonal 0.1189912

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.45190 0.43344 0.02816 0.02736 0.02343 0.00871 0.00275 0.00271 0.00271 0.00271 0.00271 0.00296 0.00502 0.00271 0.00271 $SM Pr_somatic_clonal 0.8631397

$GL [1] 0

$SC Pr_subclonal 0.1368603

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.39518 0.40905 0.04986 0.05235 0.02905 0.02295 0.01578 0.00359 0.00289 0.00289 0.00289 0.00315 0.00458 0.00289 0.00289 $SM Pr_somatic_clonal 0.9020224

$GL [1] 0

$SC Pr_subclonal 0.09797764

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.57772 0.36127 0.01991 0.00907 0.00279 0.00271 0.00271 0.00272 0.00480 0.00271 0.00271 0.00271 0.00271 0.00271 0.00271 $SM Pr_somatic_clonal 0.7620057

$GL [1] 0

$SC Pr_subclonal 0.2379943

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.63175 0.31012 0.02115 0.00480 0.00282 0.00282 0.00282 0.00397 0.00282 0.00282 0.00282 0.00282 0.00282 0.00282 0.00282 $SM Pr_somatic_clonal 0.7142293

$GL [1] 0

$SC Pr_subclonal 0.2857707

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.45329 0.43463 0.02744 0.02595 0.02314 0.00867 0.00273 0.00270 0.00270 0.00270 0.00270 0.00295 0.00500 0.00270 0.00270 $SM Pr_somatic_clonal 0.861933

$GL [1] 0

$SC Pr_subclonal 0.138067

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.72984 0.21368 0.00407 0.00765 0.00407 0.00407 0.00407 0.00407 0.00407 0.00407 0.00407 0.00407 0.00407 0.00407 0.00407 $SM Pr_somatic_clonal 0.3290336

$GL [1] 0

$SC Pr_subclonal 0.6709664

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.61972 0.30083 0.00611 0.00611 0.00611 0.00611 0.00611 0.00611 0.00611 0.00611 0.00611 0.00611 0.00611 0.00611 0.00611 $SM Pr_somatic_clonal 0.08670853

$GL [1] 0

$SC Pr_subclonal 0.9132915

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.61766 0.30246 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 $SM Pr_somatic_clonal 0.08123675

$GL [1] 0

$SC Pr_subclonal 0.9187633

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.61766 0.30246 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 0.00614 $SM Pr_somatic_clonal 0.07705511

$GL [1] 0

$SC Pr_subclonal 0.9229449

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.69683 0.25705 0.01058 0.00294 0.00294 0.00294 0.00323 0.00294 0.00294 0.00294 0.00294 0.00294 0.00294 0.00294 0.00294 $SM Pr_somatic_clonal 0.643543

$GL [1] 0

$SC Pr_subclonal 0.356457

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.56450 0.38500 0.01523 0.00276 0.00276 0.00276 0.00276 0.00276 0.00490 0.00276 0.00276 0.00276 0.00276 0.00276 0.00276 $SM Pr_somatic_clonal 0.8053071

$GL [1] 0

$SC Pr_subclonal 0.1946929

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

.som_theta_Q_MAP: [1] 0.75042 0.20422 0.00347 0.00327 0.00594 0.00327 0.00327 0.00327 0.00327 0.00327 0.00327 0.00327 0.00327 0.00327 0.00327 $SM Pr_somatic_clonal 0.5144962

$GL [1] 0

$SC Pr_subclonal 0.4855038

$OL [1] 0.001

$Pi_SM [1] 15

$Pi_SC [1] 15

. -> RunAbsolute done. Retrieving results... --> Files in cache directory: [1] "TCGA-DK-A1A6-01.ABSOLUTE.RData" "TCGA-DK-A1A6-01.ABSOLUTE_plot.pdf" "TCGA-DK-A1A6-06.ABSOLUTE.RData"
[4] "TCGA-DK-A1A6-06.ABSOLUTE_plot.pdf" "TCGA-DK-A1A6-10.ABSOLUTE.RData" "TCGA-DK-A1A6-10.ABSOLUTE_plot.pdf" [7] "tmp"
-> Checking result files... -> Checked. -> Running Absolute summarize... ... -> Absolute summarize done. Prepare auto-reviewing... -> Absolute Auto-reviewing done. -> Outputing final results... --> Choose keeping all results... Directory test/seg does not exists. Directory test/maf does not exists. --> Copying DoAbsolute files in review dir to result directory... --> Copying C:\Users\MIAOCU~1\AppData\Local\Temp\RtmpO6Tman/Absolute/cache/review/reviewed/SEG_MAF/TCGA-DK-A1A6-01.segtab.txt, C:\Users\MIAOCU~1\AppData\Local\Temp\RtmpO6Tman/Absolute/cache/review/reviewed/SEG_MAF/TCGA-DK-A1A6-06.segtab.txt to test/seg ... --> Copying C:\Users\MIAOCU~1\AppData\Local\Temp\RtmpO6Tman/Absolute/cache/review/reviewed/SEG_MAF/TCGA-DK-A1A6-01_ABS_MAF.txt, C:\Users\MIAOCU~1\AppData\Local\Temp\RtmpO6Tman/Absolute/cache/review/reviewed/SEG_MAF/TCGA-DK-A1A6-06_ABS_MAF.txt to test/maf ... Directory test/summary does not exists. Directory test/sample_before_summary does not exists. Directory test/sample_final_called does not exists.

ShixiangWang commented 4 months ago

It should be the installation problem of a correct ABSOLUTE version. I am closing this now. Please file another issue if you found new use problem.